Population Genomics of Plasmodium Species

Population genomics of Plasmodium species harnesses high-throughput sequencing to investigate the genetic diversity, evolutionary trajectories and transmission networks of malaria parasites at a population level. By comparing genomes from geographically and temporally diverse isolates, researchers can infer origins of outbreaks, patterns of parasite migration and the emergence of drug-resistance alleles. Whole-genome sequencing and targeted genotyping approaches reveal the degree of relatedness among infections, distinguishing new introductions from relapses or recrudescence. Insights into population structure clarify how ecological factors, vector biology and human movement shape parasite diversity. Moreover, characterising selective sweeps in resistance-associated loci and multigene families underpins informed strategies for surveillance, control and elimination. Advances in analytical frameworks, from identity-by-descent mapping to coalescent modelling, provide quantitative estimates of transmission intensity and historical demography. The integration of genomic data into public health programmes promises to refine diagnostic tools, guide therapeutic policy and monitor the impact of interventions in real time, underpinning efforts towards malaria eradication on a global scale.

Research from Nature Portfolio

Recent studies have established microhaplotype panels to resolve recurrence classification and transmission dynamics of Plasmodium vivax. A global set of multi-allelic markers optimises identity-by-descent estimation, enabling accurate distinction between relapse, recrudescence and reinfection, while predicting geographic origin and detecting local outbreak events. Investigations of the re-emergence of P. vivax on Aneityum Island after elimination highlighted multiple reintroductions as key drivers of resurgence. Microsatellite genotyping and phylogenetic analyses revealed limited diversity consistent with expansion from recent founders, alongside minor contributions from neighbouring islands and potential relapses. In Ethiopia, genomic analyses of 137 P. vivax isolates uncovered high prevalence of gene amplifications in erythrocyte binding proteins and signatures of positive selection proximal to chloroquine resistance loci. Variable levels of within-host identity by descent demonstrated frequent co-transmission events, and gene flow patterns suggested that non-geographic factors modulate parasite connectivity across districts.

Population Genomics of Plasmodium Species publication trend

The graph below shows the total number of articles in population genomics of plasmodium species across all publications each year (not limited to Nature Index journals).

Technical terms

Whole-genome sequencing: Decoding of an organism’s complete DNA sequence to reveal genetic variation across its entire genome.

Identity-by-descent (IBD): Genetic segments shared between individuals inherited from a common ancestor, used to infer relatedness.

Microhaplotype: A small genomic region containing multiple linked alleles that serve as high-resolution markers for genetic diversity.

Polyclonal infection: Presence of multiple genetically distinct parasite strains within a single host.

Selective sweep: Reduction of genetic variation in a genomic region due to rapid fixation of beneficial mutations under selection.

Population structure: Non-random distribution of genetic variation across populations, reflecting historical, ecological and demographic processes.

References

1. Lineage-informative microhaplotypes for recurrence classification and spatio-temporal surveillance of Plasmodium vivax malaria parasites. Nature Communications (2024).
2. Tracing the origins of Plasmodium vivax resurgence after malaria elimination on Aneityum Island in Vanuatu. Communications Medicine (2024).
3. Genomic analysis of Plasmodium vivax describes patterns of connectivity and putative drivers of adaptation in Ethiopia. Scientific Reports (2023).
4. Rapid profiling of Plasmodium parasites from genome sequences to assist malaria control. Genome Medicine (2023).
5. Population-based genomic study of Plasmod ium vivax malaria in seven Brazilian states and across South America. The Lancet Regional Health - Americas (2023).
6. Genomic exploration of the journey of Plasmodium vivax in Latin America. PLOS Pathogens (2025).